Use isinstance(object, (types)) pattern instead of type(object) == types.Type

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index c8fa9d23021a0de0a7acbbc52fce5cfd2a7d1c99..26ff2d1cec0dab22467e97b9b486d0fe554459f3 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -7,8 +7,7 @@ from optparse import OptionParser, IndentedHelpFormatter
 import os
 import sys
 import types
-import urllib
-import urllib2
+import six
 
 try:
     import json
@@ -403,12 +402,11 @@ def format_pooled_libraries(shared, library):
     sequences = library.get('index_sequence', None)
     if sequences is None:
         return []
-    elif (type(sequences) in types.StringTypes and
-          sequences.lower().startswith('err')):
+    elif isinstance(sequences, six.string_types):
         shared['Index'] = ''
         shared['SampleProject'] = library['library_id']
         return [shared]
-    elif (type(sequences) == types.DictType):
+    elif isinstance(sequences, dict):
         pooled = []
         multiplex_ids = sequences.keys()
         multiplex_ids.sort(key=natural_sort_key)

diff --git a/htsworkflow/pipelines/sequences.py b/htsworkflow/pipelines/sequences.py
index 17e65cf91d6ce9f848ca18947ee2ed279e8b3c8c..1d746c9844f8a82a15a586f76b8baa65dd594b9a 100644 (file)
--- a/htsworkflow/pipelines/sequences.py
+++ b/htsworkflow/pipelines/sequences.py
@@ -7,6 +7,7 @@ import os
 import types
 import re
 import sys
+import six
 from six.moves.urllib.parse import urljoin, urlparse
 
 import RDF
@@ -376,7 +377,7 @@ def scan_for_sequences(dirs):
     Scan through a list of directories for sequence like files
     """
     sequences = []
-    if type(dirs) in types.StringTypes:
+    if isinstance(dirs, six.string_types):
         raise ValueError("You probably want a list or set, not a string")
 
     for d in dirs:

diff --git a/htsworkflow/pipelines/summary.py b/htsworkflow/pipelines/summary.py
index c1108a2e83abf25661bcf779f44bd87e3c7cca74..8c3ec7747b551e011fae474ef257f9a276a7ba69 100644 (file)
--- a/htsworkflow/pipelines/summary.py
+++ b/htsworkflow/pipelines/summary.py
@@ -6,7 +6,6 @@ from __future__ import print_function, unicode_literals
 import os
 import logging
 import re
-import types
 from pprint import pprint
 
 from lxml import html
@@ -287,8 +286,7 @@ class LaneResultSummary(object):
             value = getattr(self, variable_name)
             if value is None:
                 continue
-            # it looks like a sequence
-            elif type(value) in (types.TupleType, types.ListType):
+            elif isinstance(value, (tuple, list)):
                 element = make_mean_range_element(
                   lane_result,
                   tag,

diff --git a/htsworkflow/submission/condorfastq.py b/htsworkflow/submission/condorfastq.py
index 705d47e0412587b287010985c90b2469f325cca2..8c35e57f88aae3984c202c35dde01f18a263de99 100644 (file)
--- a/htsworkflow/submission/condorfastq.py
+++ b/htsworkflow/submission/condorfastq.py
@@ -5,6 +5,7 @@ import os
 from pprint import pformat,pprint
 import sys
 import types
+import six
 from six.moves.urllib.parse import urljoin, urlparse
 
 from htsworkflow.pipelines.sequences import scan_for_sequences, \
@@ -335,7 +336,7 @@ class SequenceResult(object):
         self.cycle = fromTypedNode(result['cycle'])
         self.lane_number = fromTypedNode(result['lane_number'])
         self.read = fromTypedNode(result['read'])
-        if type(self.read) in types.StringTypes:
+        if isinstance(self.read, six.string_types):
             self.read = 1
         self.library = result['library']
         self.library_id = fromTypedNode(result['library_id'])

diff --git a/htsworkflow/submission/daf.py b/htsworkflow/submission/daf.py
index b2d7419784e0ebf257b688b9867cecdfee3bed22..90993def35d8058618325fdf9d0c114f527e7e19 100644 (file)
--- a/htsworkflow/submission/daf.py
+++ b/htsworkflow/submission/daf.py
@@ -1,5 +1,6 @@
 """Parse UCSC DAF File
 """
+import collections
 import logging
 import os
 from pprint import pformat
@@ -265,7 +266,7 @@ class UCSCSubmission(object):
         else:
             self.model = get_model()
 
-        if hasattr(daf_file, 'next'):
+        if isinstance(daf_file, collections.Iterable):
             # its some kind of stream
             self.daf = daf_file.read()
         else:

diff --git a/htsworkflow/submission/encoded.py b/htsworkflow/submission/encoded.py
index 334a03f24db2ec7945aa34d94aff41cdc60c8df0..5a7866f7c35cde54f73f33b4f5ea0e85ffcab12f 100644 (file)
--- a/htsworkflow/submission/encoded.py
+++ b/htsworkflow/submission/encoded.py
@@ -11,7 +11,7 @@ import json
 import jsonschema
 import os
 import requests
-import types
+import six
 from six.moves.urllib.parse import urljoin, urlparse, urlunparse
 
 LOGGER = logging.getLogger(__name__)
@@ -132,7 +132,7 @@ class ENCODED:
         and I needed a way to properly compute a the correct base URL.
         '''
         # pretend strings aren't iterable
-        if type(obj) in types.StringTypes:
+        if isinstance(obj, six.string_types):
             return
 
         # recurse on container types
@@ -223,7 +223,7 @@ class ENCODED:
         obj_type = obj.get('@type')
         if not obj_type:
             raise ValueError('None type')
-        if type(obj_type) in types.StringTypes:
+        if isinstance(obj_type, six.string_types):
             raise ValueError('@type should be a list, not a string')
         if not isinstance(obj_type, collections.Sequence):
             raise ValueError('@type is not a sequence')

diff --git a/htsworkflow/util/rdfhelp.py b/htsworkflow/util/rdfhelp.py
index ea1020c7b28fde8e4213b960afb7b90233d40300..ebd2d2695781a5166d2955aefdc2be9375a5af9d 100644 (file)
--- a/htsworkflow/util/rdfhelp.py
+++ b/htsworkflow/util/rdfhelp.py
@@ -5,6 +5,7 @@ from __future__ import print_function
 import collections
 from datetime import datetime
 from glob import glob
+import six
 from six.moves import urllib
 import logging
 import os
@@ -78,7 +79,7 @@ def blankOrUri(value=None):
     node = None
     if value is None:
         node = RDF.Node()
-    elif type(value) in types.StringTypes:
+    elif isinstance(value, six.string_types):
         node = RDF.Node(uri_string=value)
     elif isinstance(value, RDF.Node):
         node = value
@@ -89,16 +90,16 @@ def blankOrUri(value=None):
 def toTypedNode(value, language="en"):
     """Convert a python variable to a RDF Node with its closest xsd type
     """
-    if type(value) == types.BooleanType:
+    if isinstance(value, bool):
         value_type = xsdNS['boolean'].uri
         if value:
             value = u'1'
         else:
             value = u'0'
-    elif type(value) in (types.IntType, types.LongType):
+    elif isinstance(value, int):
         value_type = xsdNS['decimal'].uri
         value = unicode(value)
-    elif type(value) == types.FloatType:
+    elif isinstance(value, float):
         value_type = xsdNS['float'].uri
         value = unicode(value)
     elif isinstance(value, datetime):
@@ -252,7 +253,7 @@ def get_model(model_name=None, directory=None, use_contexts=True):
 
 
 def load_into_model(model, parser_name, path, ns=None):
-    if type(ns) in types.StringTypes:
+    if isinstance(ns, six.string_types):
         ns = RDF.Uri(ns)
 
     if isinstance(path, RDF.Node):
@@ -304,7 +305,7 @@ def load_string_into_model(model, parser_name, data, ns=None):
 def fixup_namespace(ns):
     if ns is None:
         ns = RDF.Uri("http://localhost/")
-    elif type(ns) in types.StringTypes:
+    elif isinstance(ns, six.string_types):
         ns = RDF.Uri(ns)
     elif not(isinstance(ns, RDF.Uri)):
         errmsg = "Namespace should be string or uri not {0}"

diff --git a/htsworkflow/util/test/test_rdfhelp.py b/htsworkflow/util/test/test_rdfhelp.py
index 2ea38daa6966a1956af54167c0a0dba4c669fd2c..c71d3d76899c04e0ea9e6afa3413d8d6366cd566 100644 (file)
--- a/htsworkflow/util/test/test_rdfhelp.py
+++ b/htsworkflow/util/test/test_rdfhelp.py
@@ -3,8 +3,8 @@ from __future__ import print_function
 import os
 import types
 from unittest import TestCase
-
 from datetime import datetime
+import six
 
 from htsworkflow.util.rdfhelp import \
      add_default_schemas, \
@@ -69,7 +69,7 @@ try:
             s = "Argh matey"
             node = toTypedNode(s)
             self.assertEqual(fromTypedNode(node), s)
-            self.assertEqual(type(fromTypedNode(node)), types.UnicodeType)
+            self.assertTrue(isinstance(fromTypedNode(node), six.text_type))
 
         def test_blank_or_uri_blank(self):
             node = blankOrUri()
@@ -90,8 +90,7 @@ try:
         def test_unicode_node_roundtrip(self):
             literal = u'\u5927'
             roundtrip = fromTypedNode(toTypedNode(literal))
-            self.assertEqual(roundtrip, literal)
-            self.assertEqual(type(roundtrip), types.UnicodeType)
+            self.assertTrue(isinstance(roundtrip, six.text_type))
 
         def test_datetime_no_microsecond(self):
             dateTimeType = xsdNS['dateTime'].uri

diff --git a/samples/models.py b/samples/models.py
index 94cd075bd641b2ad949b080a253289e31549236d..eaa433b7f86caf6367b3d036e8805cba96f8bdf4 100644 (file)
--- a/samples/models.py
+++ b/samples/models.py
@@ -7,6 +7,7 @@ from django.contrib.auth.models import User, UserManager
 from django.core import urlresolvers
 from django.db.models.signals import pre_save, post_save
 from django.db import connection
+import six
 
 logger = logging.getLogger(__name__)
 
@@ -281,7 +282,7 @@ class Library(models.Model):
       sequences = self.index_sequences()
       if sequences is None:
           return ""
-      if type(sequences) in types.StringTypes:
+      if isinstance(sequences, six.string_types):
           return sequences
       multiplex_ids = sequences.keys()
       multiplex_ids.sort()